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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialDE
###
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* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* preparing ‘spatialDE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spatialDE.Rmd’ using rmarkdown
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/spatialDE/1.13.0/env

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.6-h2dba641_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 
  liblzma            conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package scipy-1.9.3-py38h8ce737c_0 requires python_abi 3.8.* *_cp38, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ python 3.12.8**  is installable and it requires
│  └─ python_abi 3.12.* *_cp312, which can be installed;
└─ scipy 1.9.3**  is not installable because there are no viable options
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
   └─ scipy 1.9.3 would require
      └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.


Quitting from spatialDE.Rmd:122-125 [stabilize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
    ▆
 1. └─spatialDE::stabilize(Rep11_MOB_0)
 2.   └─basilisk::basiliskStart(spatialDE_env, testload = "scipy.optimize")
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::conda_install(...)
 6.           └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘spatialDE.Rmd’

SUMMARY: processing the following file failed:
  ‘spatialDE.Rmd’

Error: Vignette re-building failed.
Execution halted